Sequence
atgc intronic sequence ATGC exonic sequence...attacattatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacataggttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
Basic information
species | Glycine max |
transcript | GLYMA15G16270.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 11
--------attacattatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacataggttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
|| | || ||| | | | | || |||| | |||| | ||| || | ||| || ||| | || || |||| ||||| || || |||||||||| |||||||| | ||||| |||| ||||||||||||||||||| ||||||||||| || || ||| | ||
gatatgcttgtatactaaattactaaactaacattagaaaccattataat---aattgcatcaaataa-ttctagtaagttaatgaatttatat--tttggtt--cagGTAATTAGAAGTGTTGGTCAATGGTCAGCTGGAACCACTCAAATCGAAGGAAGCATCCACAATGCCTATTTTTCTCTTATTGAAAAGGCAGAACATTTTG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 10
--attacat-tatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacataggttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
|| | | ||| || || | | |||| | | || |||| || | | | | |||| || || | ||||| || | || || ||| ||||| || ||||||| ||||| ||||| |||||||||||||||||||| ||||| || || ||||| ||| | ||
atgttgcttgtatagtaacactaaaaaacaaatagaaattattttcaactgtattatacatgtgtggctaatcaaacacacattttaaattttaactc---agGTTGTTCGAAGTGTTGGTCCGTGGTCAGCAGGAACAACTCAAATTGAAGGGAGCATCCACAATGCCTATTTTTCTCTCATCGAAAAAGCAGAACATTTTG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 11
attacattatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacataggttgttgtattt---tctctcattaaaata--accaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
| |||| | | | ||| ||| | || | || |||||| |||| ||||| |||| | | | || || | | ||||| ||||||| || |||||||||| ||||| || | ||||| ||||| ||||||||||||||||| | ||||| |||||||| || ||| |||||
aagacatg--cctgtacgcttttttcacctcgaacggaca-tgtgtattttt--gcatacattgttttattgaagtattttatgaatgtgtgatttttcgctcagGTTGTTAGGAGTGTCGGTCAATGGTCAGCTGGGACCACTCAAATTGAAGGAAGCATCCACAATGCCTACTTTTCTCTGATTGAGAAGGCAGAACACTTCG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 13
-attacattatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacatag-gttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
||| ||| || | || | | | | | || | ||||||| ||| || || || || ||| || | | | | | |||||||||||||||| ||||| ||||||||||||||||| ||| |||||| |||| || ||||| |||||||| ||||| || || || ||| |||| |
aatttatatatgttgtcactctag--catatttatgggattgaatccttttttcattataatattatttgtttaactatcagaaataatatctcactttcagGTTATTAGGAGCGTCAGTCAGTGGTCTGCTGGAACAAGCCAAGTTGAAGACAGCACTCATAATGCTTATTGCTCCCTTATAGAAAAGGCAGAACACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttttcaacataggttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
aaataac putative branch site (score: 2)
tattttctctcattaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attacattatcttatttcttttgttctcgtcacttttatgctgccaatttttcaacataggttgttgtattttctctcattaaaataaccaaattgatagGTTATTAGGAGCGTAAGTCAATGGTCTGCTGGAACAAGTCAAACTGAAGAGAGCATCCACAATGCCTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - -atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa